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Function TypeShort Function NameLong Function NameEvaluatedCredited GivenFunction accepted in placeEvaluation LevelExamplesComments
Abundances




a()
abundance()YESOnly together with correct namespace and identifierTerm-level Used with CHEBI namespace
complex()
complexAbundance()YESYESFunction-level
 complex(p(HGNC:FOS),p(HGNC:JUN))   
All arguments of the complex() function are expected. Partial is credit is given if arguments are missing or if placeholders are used.
composite()
compositeAbundance()NONO Not present in testset
g()
geneAbundance()YES

as g() and as p()

Only together with correct namespace and identifier

p()optional replacementTerm-level

 

We recommend to use p() instead
m()
microRNAAbundance()YES

as m() and as p()

Only together with correct namespace and identifier

p()optional replacementTerm-level We recommend to use p() instead
p()
proteinAbundance()YES

YES

Only together with correct namespace and identifier

Term-level Used with the following namespaces: HGNC, MGI, EGID
r()
rnaAbundance()YES

as r() and as p()

Only together with correct namespace and identifier

p()optional replacementTerm-level We recommend to use p() instead
Modifications


f()
fusion()NO Not in dataset
pmod()
proteinModification()YESYESFunction-level

Original Statement (accepted):

p(HGNC:MMP2) increases p(HGNC:AKT1,pmod(P,S,473))

Simplified Statement (also accepted):

p(HGNC:MMP2) increases p(HGNC:AKT1,pmod(P))

Only the P argument is obligatory.

Additional arguments are treated as optional (not credit is given) but must be syntactically correct if provided.

sub()
substitution()NONO Not present in testset
trunc()
truncation()NONO Not present in testset
Processes
bp()
biologicalProcess()YESYESTerm-level Used with GOBP namespace
path()
pathology()YESYESTerm-level Used with MESHD namespace
Transformations



sec()
cellSecretion()YESonly as tloc()tloc()obligatory replacementFunction-level tloc() function must be used instead
surf()
cellSurfaceExpression()YESonly as tloc()tloc()obligatory replacementFunction-level tloc() function must be used instead
deg()
degradation()YESYESFunction-level  
rex()
reaction()NONO Not present in testset
tloc()
translocation()YESYESFunction-level Location arguments are treated as optional
Activities








cat()
catalyticActivity()YESonly as act()act()obligatory replacementFunction-level

Original Statement (not accepted):

p(HGNC:WNT5B) increases cat(p(HGNC:FZD6)

Simplified Statement (accepted):

p(HGNC:WNT5B) increases act(p(HGNC:FZD6)
act() function must be used instead
chap()
chaperoneActivity()YESonly as act()act()obligatory replacementFunction-level

Original Statement (not accepted):

p(MGI:Clgn) increases chap(p(MGI:Clgn))

Simplified Statement (accepted):

p(MGI:Clgn) increases act(p(MGI:Clgn))
act() function must be used instead
gtp()
gtpBoundActivity()YESonly as act()act()obligatory replacementFunction-level

Original Statement (not accepted):

p(HGNC:TIAM1) increases gtp(p(HGNC:RAC1))

Simplified statement (accepted):

p(HGNC:TIAM1) increases act(p(HGNC:RAC1))
act() function must be used instead
kin()
kinaseActivity()YESonly as act()act()obligatory replacementFunction-level

 

act() function must be used instead
act()
molecularActivity()YESYES obligatory replacementFunction-level

Original Statement (not accepted):

kin(p(MGI:Kdr)) increases bp(GOBP:"blood vessel development")

Simplified statement (accepted):

act(p(MGI:Kdr)) increases bp(GOBP:"blood vessel development")
 
pep()
pepdidaseActivity()YESonly as act()act()obligatory replacementFunction-level

Original Statement (not accepted):

r(MGI:Fbln5) decreases pep(p(HGNC:MMP2))

Simplified statement (accepted):

r(MGI:Fbln5) decreases act(p(HGNC:MMP2))
act() function must be used instead
phos()
phosphataseActivity()YESonly as act()act()obligatory replacementFunction-level

Original Statement (not accepted):

tscript(p(MGI:Rbl1)) decreases phos(p(MGI:Alpl))

Simplified Statement (accepted):

act(p(MGI:Rbl1)) decreases act(p(MGI:Alpl))
act() function must be used instead
ribo()
ribosylationActivity()NONO  Not present in testset
tscript()
transcriptionalActivity()YESonly as act()act()obligatory replacementFunction-level

Original Statement (not accepted):

cat(p(HGNC:F2)) increases tscript(p(HGNC:JUN))

Simplified statement (accepted):

act(p(HGNC:F2)) increases act(p(HGNC:JUN))
act() function must be used instead
tport()
transportActivity()YESonly as act()act()obligatory replacementFunction-level

Original Statement (not accepted):

tport(p(HGNC:CFTR)) decreases a(CHEBI:glutathione)

Simplified statement (accepted):

act(p(HGNC:CFTR)) decreases a(CHEBI:glutathione)
act() function must be used instead
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